I have installed BWA. And build index of hg19 using command:
bwa index -a bwtsw hg19.fa
Now I find alignment using command:
./bwa aln hg19.fa SRR44930951.fastq > alnsa.sai
However, I want to find alignments allowing 1 or 2 mismatches.
From BWA home page, I found, I have to use XM tag.
But, can't get how to use that means what should be the command.
Can anybody please help me on this ?